Your example is (unfortunately) far too complex for me to answer your substantive question, but the sub-question "Why does \hyp[h]enation {/word/} inline [cause] the whole /word/ [to] disappear ?" is much easier to answer.
\hyphenation {<word>} tells TeX how to hyphenate subsequent occurrences of <word> in the text; it does not expand to a word with valid hyphenation points embedded but rather expands to the empty set.
Philip Taylor
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